This review addresses the quantification of anthropogenic pollutants in lacustrine sediments by multidisciplinary analyses including: chronostratigraphy using radioisotopes (137Cs) and radiocarbon dates (14C), trace metal analysis, faecal indicator analysis, as well as antibiotic-resistant genes by molecular analysis. Sediment cores from lakes Lucerne and Geneva that are located at a distance of 150 km from each other reveal a synchronous increase in anthropogenic trace metals (Pb, Cu, Zn, and Mn) following the industrial revolution in Europe about 1850. In both lakes, the peak of water pollution by toxic metals due to discharge of industrial wastewaters was reached in the middle of the twentieth century. During the second part of the twentieth century, both sites show a decrease in metal pollution following the implementation of wastewater treatment plants. On the contrary, the Vidy Bay of Lake Geneva where the treated wastewaters from the city of Lausanne are released since 1964 points out a dramatic increase in trace metal deposition. Later, a high increase in organic matter deposition, in bacteria (Escherichia coli and Enterococcus faecalis) activity as well as antibiotic-resistant genes and bacteria occurred into the bay, simultaneously with the eutrophication of the large and deep perialpine lakes in the 1970s due to excessive external nutrient loading.